PDB
5L7I
Resolution
3.3 Å
Released
July 20, 2016
Receptor
SMO
Class
F
Species
Homo sapiens
Ligand
vismodegib
Function
Antagonist
Reference
10.1038/NATURE18934

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Ligand Amino Acid Generic Number Segment Interaction Type
vismodegib W281 2.58x58 TM2 aromatic (edge-to-face)
vismodegib V386 ECL2 hydrophobic
vismodegib Y394 ECL2 polar (hydrogen bond)
vismodegib Y394 ECL2 Van der Waals
vismodegib H470 6.51x51 TM6 Van der Waals
vismodegib D473 6.54x54 TM6 polar (charge-assisted hydrogen bond)
vismodegib Q477 6.58x58 TM6 Van der Waals
vismodegib W480 6.61x61 TM6 hydrophobic
vismodegib W480 6.61x61 TM6 Van der Waals
vismodegib P513 ECL3 hydrophobic
vismodegib P513 ECL3 Van der Waals
vismodegib E518 7.38x38 TM7 polar (charge-assisted hydrogen bond)
vismodegib N521 7.41x41 TM7 Van der Waals
vismodegib L522 7.42x42 TM7 hydrophobic
vismodegib L522 7.42x42 TM7 Van der Waals
vismodegib M525 7.45x45 TM7 Van der Waals

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Snake plot — Download: PNG | SVG
ICL1 W R N S N ICL1ECL1 M D G A R R E I V C R A D G T M R L G E P T S N E T ECL1ICL2 L G T T Y Q P L S G ICL2ECL2 Q V D G D S V S G I C F V G Y K ECL2ICL3 P G L L ICL3ECL3 G L P T K Q P I P D C E I K N R P ECL3N-term M A A A R P A R G P E L P L L G L L L L L L L G D P G R G A A S S G N A T G P G P R S A G G S A R R S A A V T G P P P P L S H C G R A A P C E P L R Y N V C L G S V L P Y G A T S T L L A G D S D S Q E E A H G K L V L W S G L R N A P R C W A V I Q P L L C A V Y M P K C E N D R V E L P S R T L C Q A T R G P C A I V E R E R G W P D F L R C T P D R F P E G C T N E V Q N I K F N S S G Q C E V P L V R T D N P K S W Y E D V E G C G I Q C Q N P L F N-termC-term G Q S D D E P K R I K K S K M I A K A F S K R H E L L Q N P G Q E L S F S M H T V S H D G P V A G L A F D L N E P S A D V S S A W A Q H V T K M V A R R G A I L P Q D I S V T P V A T P V P P E E Q A N L W L V E A E I S P E L Q K R L G R K K K R R K R K K E V C P L A P P P E L H P P A P A P S T I P R L P Q L P R Q K C L V A A G A W G A G D S C R Q G A W T L V S N P F C P E P S P P Q D P F L P S A P A P V A W A H G R R Q G L G P I H S R T N L M D T E L M D A D S D F C-term T E A E H Q D M H S Y I A A F G A V T G L C T L F T L A T F V A D R Y P A V I L F Y V N A C F F V G S I G W L A Q F L S C V I I F V I V Y Y A L M A G V V W F V V L T Y A W H T S F K A K T S Y F H L L T W S L P F V L T V A I L A V A N Y R Y R A G F V L A P I G L V L I V G G Y F L I R G V M T L F S I K S N H S E K A A S K I N E T M L R L G I F G F L A F G F V L I T F S C H F Y D F F N Q A E W E R S F R D Y V L C Q A N V T I S L L V E K I N L F A M F G T G I A M S T W V W T K A W R R L T T L L I T W C R
Helix box plot — Download: PNG | SVG L T C L G T V A G F A A I Y S H M D Q H 1 F Y V N A C F F V G S I G W L A Q F 2 V V F W V V G A M L A Y Y V I V F I I V 3 T S Y F H L L T W S L P F V L T V A I L 4 L F Y G G V I L V L G I P A L V F G A R Y 5 G I F G F L A F G F V L I T F S C H F Y 6 T S M A I G T G F M A F L N I K E V L L 7

GPCRdb(A)
GPCRdb(F)
SMO
TM2
2x57 2.58x58 W281
TM6
6x55 6.51x51 H470
6x58 6.54x54 D473
6x62 6.58x58 Q477
6x65 6.61x61 W480
TM7
7x35 7.38x38 E518
7x38 7.41x41 N521
7x39 7.42x42 L522
7x42 7.45x45 M525